GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acn in Pseudomonas fluorescens FW300-N2C3

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate AO356_24390 AO356_24390 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase

Query= BRENDA::P36683
         (865 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 AO356_24390
           bifunctional aconitate hydratase 2/2-methylisocitrate
           dehydratase
          Length = 869

 Score = 1377 bits (3563), Expect = 0.0
 Identities = 667/859 (77%), Positives = 761/859 (88%), Gaps = 3/859 (0%)

Query: 1   MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
           +LE YRKH+ ERAA GI P+PL+A Q A L+ELLKNPPAGEE FL+DL+TNRVPPGVDEA
Sbjct: 1   VLEAYRKHIEERAALGIVPQPLNAEQTAGLIELLKNPPAGEEAFLVDLITNRVPPGVDEA 60

Query: 61  AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
           AYVKAGFL+A+AKG+A+SPLL  ++A+ELLGTMQGGYNI  L++ LDDA+LAP+AAK L 
Sbjct: 61  AYVKAGFLSALAKGQAQSPLLDKKRAVELLGTMQGGYNIVTLVELLDDAELAPVAAKELK 120

Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
           HTLLMFD F+DV EKAK GN +AK V+QSWAD EWF NRP LA+K+++ VFKVTGETNTD
Sbjct: 121 HTLLMFDAFHDVAEKAKNGNVHAKAVLQSWADGEWFKNRPVLADKISLRVFKVTGETNTD 180

Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
           DLSPAPDAWSRPDIPLHALAMLK AR+GI PD+ G  GP+KQIE ++ +GFP+AYVGDVV
Sbjct: 181 DLSPAPDAWSRPDIPLHALAMLKMARDGIVPDEQGKTGPMKQIEEMRGQGFPIAYVGDVV 240

Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
           GTGSSRKSATNSVLWF GDD+P VPNKR GG C G KIAPIF+NTMEDAGALPIE DVSN
Sbjct: 241 GTGSSRKSATNSVLWFFGDDVPFVPNKRAGGFCFGSKIAPIFYNTMEDAGALPIEFDVSN 300

Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
           ++MGDVID+YP+ G+V  H T E+L TFE+KT VL+DEVRAGGRIPLIIGRGLT KAR  
Sbjct: 301 MHMGDVIDLYPHAGKVCKHGTDEVLTTFEMKTPVLLDEVRAGGRIPLIIGRGLTEKARAE 360

Query: 361 LGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGV---KGIRPGAYCEPKMTSVGSQDTT 417
           LGLP  D+F++ +  AES +GF+LAQKMVG+ACG+   +G+RPG YCEPKMT+VGSQDTT
Sbjct: 361 LGLPAFDLFKKPEAPAESTKGFTLAQKMVGKACGLAEGQGVRPGTYCEPKMTTVGSQDTT 420

Query: 418 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDG 477
           GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKP+DV THHTLPDFIM RGGVSLRPGDG
Sbjct: 421 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPIDVTTHHTLPDFIMTRGGVSLRPGDG 480

Query: 478 VIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK 537
           +IHSWLNRMLLPDTVGTGGDSHTRFP+GISFPAGSGLVAFAAATGVMPLDMPES+LVRFK
Sbjct: 481 IIHSWLNRMLLPDTVGTGGDSHTRFPMGISFPAGSGLVAFAAATGVMPLDMPESILVRFK 540

Query: 538 GKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTD 597
           GKM+PGITLRDLVHAIP +AI+ GLLTVEKKGKKN FSGRILEIEGL  L +EQAFEL+D
Sbjct: 541 GKMKPGITLRDLVHAIPYFAIQNGLLTVEKKGKKNAFSGRILEIEGLEGLTLEQAFELSD 600

Query: 598 ASAERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPEL 657
           ASAERSAAGCTIKL+KE I EYL SNI LL+WMI EGYGD RTLERR Q ME W+ANP+L
Sbjct: 601 ASAERSAAGCTIKLSKESITEYLQSNITLLRWMIGEGYGDARTLERRAQAMEAWVANPQL 660

Query: 658 LEADADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHF 717
           +EADADAEYA VI+IDLADI EP+LCAPNDPDDAR LS+V GEKIDEVFIGSCMTNIGHF
Sbjct: 661 MEADADAEYAEVIEIDLADISEPVLCAPNDPDDARLLSSVAGEKIDEVFIGSCMTNIGHF 720

Query: 718 RAAGKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQA 777
           RAAGKLL+  KGQLPTRLW++PPT+MDA QLTEEGYY ++GK+GAR+E+PGCSLCMGNQA
Sbjct: 721 RAAGKLLEQVKGQLPTRLWLSPPTKMDAHQLTEEGYYGIYGKAGARMEMPGCSLCMGNQA 780

Query: 778 RVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTA 837
           RV   +TVVSTSTRNFPNRLG GANV+LASAELA+VA+++G+LPT EEY  Y  ++D  A
Sbjct: 781 RVEPNSTVVSTSTRNFPNRLGDGANVYLASAELASVASILGRLPTVEEYMEYAGKIDSMA 840

Query: 838 VDTYRYLNFNQLSQYTEKA 856
            D YRYL+F+Q++++ E A
Sbjct: 841 ADVYRYLSFDQIAEFREAA 859


Lambda     K      H
   0.317    0.136    0.400 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 2150
Number of extensions: 76
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 865
Length of database: 869
Length adjustment: 42
Effective length of query: 823
Effective length of database: 827
Effective search space:   680621
Effective search space used:   680621
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (26.2 bits)

Align candidate AO356_24390 AO356_24390 (bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase)
to HMM TIGR00117 (acnB: aconitate hydratase 2 (EC 4.2.1.3))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR00117.hmm
# target sequence database:        /tmp/gapView.2338.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00117  [M=844]
Accession:   TIGR00117
Description: acnB: aconitate hydratase 2
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
          0 1527.1   0.0          0 1526.9   0.0    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390  AO356_24390 bifunctional aconita


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390  AO356_24390 bifunctional aconitate hydratase 2/2-methylisocitrate deh
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1526.9   0.0         0         0       1     844 []       1     857 [.       1     857 [. 0.99

  Alignments for each domain:
  == domain 1  score: 1526.9 bits;  conditional E-value: 0
                                       TIGR00117   1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayv 63 
                                                     +le+yrkh+ eraa+gi p+plna+q+a l+ellkn+p++ee+fl++l+++rvppgvdeaayv
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390   1 VLEAYRKHIEERAALGIVPQPLNAEQTAGLIELLKNPPAGEEAFLVDLITNRVPPGVDEAAYV 63 
                                                     69************************************************************* PP

                                       TIGR00117  64 kagflaaiakgevksplisaeeavellgtmlggynvepliealeskdkniakaaakalsktll 126
                                                     kagfl+a+akg+++spl+  ++avellgtm+ggyn+ +l+e+l+  d+++a++aak l++tll
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390  64 KAGFLSALAKGQAQSPLLDKKRAVELLGTMQGGYNIVTLVELLD--DAELAPVAAKELKHTLL 124
                                                     ********************************************..***************** PP

                                       TIGR00117 127 vfdafddveelskt.neyakqvleswaeaewflnkeelaekitvtvfkvdgetntddlspapd 188
                                                     +fdaf+dv+e++k  n +ak vl+swa++ewf n++ la+ki+  vfkv+getntddlspapd
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 125 MFDAFHDVAEKAKNgNVHAKAVLQSWADGEWFKNRPVLADKISLRVFKVTGETNTDDLSPAPD 187
                                                     ************998************************************************ PP

                                       TIGR00117 189 aftrpdiplhalamlknkieeieq..........rikalkqkgvpvayvgdvvgtgssrksat 241
                                                     a++rpdiplhalamlk ++++i +          +i++++ +g+p+ayvgdvvgtgssrksat
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 188 AWSRPDIPLHALAMLKMARDGIVPdeqgktgpmkQIEEMRGQGFPIAYVGDVVGTGSSRKSAT 250
                                                     *********************999999************************************ PP

                                       TIGR00117 242 nsvlwflgkdipfvpnkragglvlggkiapiffntaedsgalpievdvkdlnegdvikiypyk 304
                                                     nsvlwf+g+d+pfvpnkragg+++g kiapif+nt+ed+galpie dv+++++gdvi++yp+ 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 251 NSVLWFFGDDVPFVPNKRAGGFCFGSKIAPIFYNTMEDAGALPIEFDVSNMHMGDVIDLYPHA 313
                                                     *************************************************************** PP

                                       TIGR00117 305 geitnket.evvatfklkpetlldevraggripliigrgltdkarealglsesevfkkakapa 366
                                                     g++ ++ t ev++tf++k+ +lldevraggripliigrglt+kar  lgl+  ++fkk++apa
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 314 GKVCKHGTdEVLTTFEMKTPVLLDEVRAGGRIPLIIGRGLTEKARAELGLPAFDLFKKPEAPA 376
                                                     ******9999***************************************************** PP

                                       TIGR00117 367 esakgftlaqklvgkacgv...kgirpgtycepkvttvgsqdttgamtrdelkelaslgfdad 426
                                                     es+kgftlaqk+vgkacg+   +g+rpgtycepk+ttvgsqdttg+mtrdelk+la+lgf+ad
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 377 ESTKGFTLAQKMVGKACGLaegQGVRPGTYCEPKMTTVGSQDTTGPMTRDELKDLACLGFSAD 439
                                                     ******************86668**************************************** PP

                                       TIGR00117 427 lvlqsfchtaaypkpvdvkthktlpdfisqrggvalrpgdgvihswlnrmllpdtvgtggdsh 489
                                                     lv+qsfchtaaypkp+dv th+tlpdfi++rggv+lrpgdg+ihswlnrmllpdtvgtggdsh
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 440 LVMQSFCHTAAYPKPIDVTTHHTLPDFIMTRGGVSLRPGDGIIHSWLNRMLLPDTVGTGGDSH 502
                                                     *************************************************************** PP

                                       TIGR00117 490 trfplgisfpagsglvafaaatgvmpldmpesvlvrfkgelqpgitlrdlvnaipyyaikkgl 552
                                                     trfp+gisfpagsglvafaaatgvmpldmpes+lvrfkg+++pgitlrdlv+aipy+ai++gl
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 503 TRFPMGISFPAGSGLVAFAAATGVMPLDMPESILVRFKGKMKPGITLRDLVHAIPYFAIQNGL 565
                                                     *************************************************************** PP

                                       TIGR00117 553 ltvekkgkvnvfngrileieglpdlkveqafeltdasaersaagctiklnkepvieylksniv 615
                                                     ltvekkgk+n f+grileiegl  l +eqafel+dasaersaagctikl+ke++ eyl+sni 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 566 LTVEKKGKKNAFSGRILEIEGLEGLTLEQAFELSDASAERSAAGCTIKLSKESITEYLQSNIT 628
                                                     *************************************************************** PP

                                       TIGR00117 616 llkemiaegyedkrtlkrridamekwlanpelleadadaeyaavieidlaeikepilaapndp 678
                                                     ll++mi egy+d+rtl+rr +ame+w+anp+l+eadadaeya+vieidla+i ep+l+apndp
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 629 LLRWMIGEGYGDARTLERRAQAMEAWVANPQLMEADADAEYAEVIEIDLADISEPVLCAPNDP 691
                                                     *************************************************************** PP

                                       TIGR00117 679 ddvkllsevagdaidevfigscmtnighfraagkileaak.tvkarlwvvpptrmdeqqliee 740
                                                     dd++lls vag++idevfigscmtnighfraagk+le+ k ++++rlw+ ppt+md++ql+ee
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 692 DDARLLSSVAGEKIDEVFIGSCMTNIGHFRAAGKLLEQVKgQLPTRLWLSPPTKMDAHQLTEE 754
                                                     *************************************9988********************** PP

                                       TIGR00117 741 gyyaifgaagartevpgcslcmgnqarvedgatvfststrnfdnrlgkgakvylgsaelaava 803
                                                     gyy+i+g+agar+e+pgcslcmgnqarve ++tv+ststrnf+nrlg ga+vyl+saela+va
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 755 GYYGIYGKAGARMEMPGCSLCMGNQARVEPNSTVVSTSTRNFPNRLGDGANVYLASAELASVA 817
                                                     *************************************************************** PP

                                       TIGR00117 804 allgkiptkeeylalvsekvesakdklyrylnfnelenfee 844
                                                     ++lg++pt+eey+++  + +  a d +yryl f+++ +f+e
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 818 SILGRLPTVEEYMEYAGKIDSMAAD-VYRYLSFDQIAEFRE 857
                                                     ***************8877766666.************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (844 nodes)
Target sequences:                          1  (869 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.06u 0.03s 00:00:00.09 Elapsed: 00:00:00.08
# Mc/sec: 8.37
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory